Sodium in PDB 3isd: Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch

All present enzymatic activity of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch:
2.7.7.7;

The structure of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch, PDB code: 3isd was solved by W.A.Beard, D.D.Shock, V.K.Batra, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.19 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.700, 77.640, 55.220, 90.00, 113.67, 90.00
R / Rfree (%)	19.5 / 26.2

The structure of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch also contains other interesting chemical elements:

Manganese

(Mn)

8 atoms

The binding sites of Sodium atom in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch (pdb code 3isd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch, PDB code: 3isd:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:22.1 occ:1.00 O A:THR101 2.1 18.2 1.0 O A:ILE106 2.6 15.2 1.0 O A:VAL103 2.6 18.0 1.0 O A:HOH377 2.6 29.1 1.0 O P:HOH36 2.6 28.5 1.0 OP1 P:DG9 2.6 19.9 1.0 C A:THR101 3.1 16.4 1.0 C A:VAL103 3.4 19.1 1.0 P P:DG9 3.6 17.5 1.0 C A:ILE106 3.6 17.6 1.0 O A:HOH494 3.7 27.6 1.0 OP2 P:DG9 3.7 13.7 1.0 CA A:THR101 3.7 15.9 1.0 CA A:SER104 3.9 20.2 1.0 N A:SER104 4.0 19.7 1.0 N A:VAL103 4.0 19.1 1.0 N A:ILE106 4.0 17.3 1.0 N A:ARG102 4.2 16.1 1.0 C A:ARG102 4.2 18.3 1.0 N A:GLY105 4.2 18.7 1.0 CB A:THR101 4.3 14.3 1.0 CA A:ILE106 4.3 17.4 1.0 CA A:VAL103 4.4 19.2 1.0 C A:SER104 4.5 20.5 1.0 CA A:ARG102 4.5 17.2 1.0 O5' P:DG9 4.5 22.3 1.0 N A:GLY107 4.6 16.7 1.0 O A:LEU100 4.6 13.3 1.0 O A:ARG102 4.7 20.8 1.0 CB A:ILE106 4.8 16.2 1.0 CA A:GLY107 4.8 17.5 1.0 O3' P:DC8 4.8 19.9 1.0 N A:THR101 5.0 14.8 1.0

Sodium binding site 2 out of 3 in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:31.2 occ:1.00 O A:LEU62 2.0 24.6 1.0 O A:LYS60 2.4 19.1 1.0 OP1 D:DC3 2.6 20.6 1.0 O D:HOH6 2.7 25.5 1.0 C A:LEU62 2.8 24.9 1.0 O A:VAL65 3.0 23.6 1.0 C A:LYS60 3.5 21.5 1.0 N A:PRO63 3.5 25.7 1.0 N A:LEU62 3.5 25.1 1.0 C A:LYS61 3.6 25.1 1.0 CA A:LEU62 3.7 24.2 1.0 O A:LYS61 3.7 25.5 1.0 CA A:PRO63 3.7 25.2 1.0 C A:VAL65 3.9 23.0 1.0 P D:DC3 3.9 18.8 1.0 N A:VAL65 4.1 23.6 1.0 N A:GLY64 4.2 26.5 1.0 N A:LYS61 4.3 23.8 1.0 CA A:LYS61 4.3 24.9 1.0 C A:PRO63 4.4 26.3 1.0 CA A:LYS60 4.4 20.7 1.0 CA A:VAL65 4.4 22.5 1.0 OP2 D:DC3 4.5 21.1 1.0 CB A:VAL65 4.5 20.6 1.0 CD A:LYS60 4.7 22.1 1.0 O A:ALA59 4.7 19.6 1.0 CD A:PRO63 4.8 27.8 1.0 CB A:LEU62 4.8 21.8 1.0 O5' D:DC3 4.9 20.7 1.0 O3' D:DT2 4.9 17.9 1.0 CE A:LYS60 4.9 19.3 1.0 CB A:PRO63 5.0 26.0 1.0 N A:GLY66 5.0 22.9 1.0

Sodium binding site 3 out of 3 in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ P:Na401 b:36.8 occ:1.00 O P:HOH184 2.5 32.2 1.0 N7 P:DG4 2.9 31.8 1.0 O P:HOH56 2.9 24.1 1.0 O6 P:DG4 3.8 25.9 1.0 C8 P:DG4 3.8 32.3 1.0 C5 P:DG4 3.9 29.1 1.0 C2' P:DT3 4.1 35.4 1.0 C6 P:DG4 4.2 27.9 1.0 N6 P:DA5 4.2 20.7 1.0

W.A.Beard, D.D.Shock, V.K.Batra, L.C.Pedersen, S.H.Wilson. Dna Polymerase Beta Substrate Specificity: Side Chain Modulation of the "A-Rule". J.Biol.Chem. V. 284 31680 2009.
ISSN: ISSN 0021-9258
PubMed: 19759017
DOI: 10.1074/JBC.M109.029843